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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $species_info = array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ) $local_species = 'aag' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $species_info = array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ) $local_species = 'aag' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $species_info = array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ) $local_species = 'cbr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $species_info = array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ) $local_species = 'cbr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $species_info = array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ) $local_species = 'cre' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $species_info = array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ) $local_species = 'cre' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $species_info = array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ) $local_species = 'lonja' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $species_info = array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ) $local_species = 'lonja' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $species_info = array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ) $local_species = 'lja' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $species_info = array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ) $local_species = 'lja' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $species_info = array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ) $local_species = 'mbi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $species_info = array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ) $local_species = 'mbi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $species_info = array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ) $local_species = 'mdo' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $species_info = array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ) $local_species = 'mdo' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $species_info = array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ) $local_species = 'mpo' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $species_info = array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ) $local_species = 'mpo' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $species_info = array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ) $local_species = 'mtr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $species_info = array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ) $local_species = 'mtr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $species_info = array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ) $local_species = 'mco' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $species_info = array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ) $local_species = 'mco' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $species_info = array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ) $local_species = 'ppa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $species_info = array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ) $local_species = 'ppa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $species_info = array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ) $local_species = 'pco' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $species_info = array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ) $local_species = 'pco' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $species_info = array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ) $local_species = 'sgi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $species_info = array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ) $local_species = 'sgi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $species_info = array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ) $local_species = 'sci' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $species_info = array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ) $local_species = 'sci' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ), 'gf_id' => 'HOM05D001266', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001266' ), 'data_identifier' => 'HOM05D001266', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001266', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '494', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33000' => 'bna', 'A04p11430' => 'bna', 'A06p12130' => 'bna', 'A07p19720' => 'bna', 'A07p27020' => 'bna', 'A09p60980' => 'bna', 'A10p22950' => 'bna', 'A10p22960' => 'bna', 'Aa31LG11G13520' => 'aar', 'Aa31LG4G1320' => 'aar', 'Aa31LG5G13040' => 'aar', 'Aa31LG7G730' => 'aar', 'Aa31LG9G17060' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.2536' => 'aag', 'Actinidia13664' => 'ach', 'Actinidia14882' => 'ach', 'Actinidia16645' => 'ach', 'Actinidia17631' => 'ach', 'Actinidia18268' => 'ach', 'Actinidia25490' => 'ach', 'Actinidia25491' => 'ach', 'Actinidia26299' => 'ach', 'Actinidia38381' => 'ach', 'Actinidia38382' => 'ach', 'Ah.07g204070' => 'amhyb', 'Ah.16g101860' => 'amhyb', 'AL1G28320' => 'aly', 'AL2G40340' => 'aly', 'AL3G11900' => 'aly', 'AL6G26970' => 'aly', 'AL7G52100' => 'aly', 'Aqoxy3G00319' => 'aox', 'Aqoxy7G03274' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JXR5Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R0TWK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AH6D3Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CQ5GAV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L7XJR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PSQ86Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TCIE48' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD47CB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WI1D2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4SPH8' => 'arhy', 'AT1G16190' => 'ath', 'AT1G79650' => 'ath', 'AT3G02540' => 'ath', 'AT5G16090' => 'ath', 'AT5G38470' => 'ath', 'ATR0171G001' => 'atr', 'ATR0580G066' => 'atr', 'Atru.chr1.2822' => 'acertr', 'AUR62002627' => 'cqu', 'AUR62002881' => 'cqu', 'AUR62006926' => 'cqu', 'AUR62008982' => 'cqu', 'AUR62023321' => 'cqu', 'AUR62030041' => 'cqu', 'AUR62032070' => 'cqu', 'AUR62035244' => 'cqu', 'BcaB02g06600' => 'bca', 'BcaB02g07230' => 'bca', 'BcaB02g08007' => 'bca', 'BcaB03g14501' => 'bca', 'BcaB06g27225' => 'bca', 'BcaB08g36886' => 'bca', 'BcaC01g04440' => 'bca', 'BcaC02g09649' => 'bca', 'BcaC04g18908' => 'bca', 'BcaC05g25595' => 'bca', 'BcaC08g44380' => 'bca', 'BcaC09g47707' => 'bca', 'BcaNung04174' => 'bca', 'BolC3t16280H' => 'bol', 'BolC4t26092H' => 'bol', 'BolC5t30164H' => 'bol', 'BolC6t37023H' => 'bol', 'BolC6t38136H' => 'bol', 'BolC8t52004H' => 'bol', 'BolC9t58933H' => 'bol', 'BolC9t58936H' => 'bol', 'BolC9t58937H' => 'bol', 'BraA03t12468Z' => 'bra', 'BraA04t16807Z' => 'bra', 'BraA06t24382Z' => 'bra', 'BraA07t29671Z' => 'bra', 'BraA07t30346Z' => 'bra', 'BraA09t41471Z' => 'bra', 'BraA10t44363Z' => 'bra', 'BraA10t44364Z' => 'bra', 'BraA10t44365Z' => 'bra', 'C03p40140' => 'bna', 'C04p45120' => 'bna', 'C05p14370' => 'bna', 'C06p18140' => 'bna', 'C06p29750' => 'bna', 'C08p44590' => 'bna', 'C09p60900' => 'bna', 'C09p60920' => 'bna', 'C09p60930' => 'bna', 'CAN.G1008.16' => 'can', 'CAN.G25.6' => 'can', 'CAN.G625.7' => 'can', 'CAN.G774.60' => 'can', 'CAN.G953.9' => 'can', 'CANSAT01G2966' => 'cansat', 'CANSAT64G1121' => 'cansat', 'CANSAT64G2888' => 'cansat', 'CARHR016670' => 'chi', 'CARHR073380' => 'chi', 'CARHR076540' => 'chi', 'CARHR291840' => 'chi', 'Carub.0001s1595' => 'cru', 'Carub.0002s2653' => 'cru', 'Carub.0003s0165' => 'cru', 'Carub.0007s3743' => 'cru', 'Ca_01004_v3' => 'car', 'Ca_04067_v3' => 'car', 'Ca_11180_v3' => 'car', 'CBR_g20362' => 'cbr', 'Cc00_g12400' => 'ccan', 'Cc04_g05410' => 'ccan', 'Cc07_g08860' => 'ccan', 'CDE02G3609' => 'cde', 'CDE04G0056' => 'cde', 'CDE04G3211' => 'cde', 'CDE05G0033' => 'cde', 'CDE05G0066' => 'cde', 'Cfa004170' => 'cfa', 'Cfa007930' => 'cfa', 'Cfa018605' => 'cfa', 'Ciclev10011886m.g' => 'ccl', 'Ciclev10025868m.g' => 'ccl', 'Ciclev10031777m.g' => 'ccl', 'CiPaw.01G051600' => 'cil', 'CiPaw.02G024500' => 'cil', 'CiPaw.03G060800' => 'cil', 'CiPaw.04G041200' => 'cil', 'CiPaw.04G041600' => 'cil', 'ClCG05G022800' => 'cla', 'ClCG10G012840' => 'cla', 'ClCG10G014660' => 'cla', 'COL.COLO4_05462' => 'col', 'COL.COLO4_07912' => 'col', 'COL.COLO4_30171' => 'col', 'Cpa.g.sc1.181' => 'cpa', 'Cpa.g.sc68.39' => 'cpa', 'Cre08.g366400' => 'cre', 'CsaV3_3G032680' => 'csa', 'CsaV3_3G041900' => 'csa', 'CsaV3_5G034230' => 'csa', 'CSS0012157' => 'camsi', 'CSS0013470' => 'camsi', 'CSS0017705' => 'camsi', 'CSS0022019' => 'camsi', 'CSS0032032' => 'camsi', 'CSS0032682' => 'camsi', 'CSS0033479' => 'camsi', 'CSS0034360' => 'camsi', 'CSS0036061' => 'camsi', 'CSS0037316' => 'camsi', 'CSS0039379' => 'camsi', 'CSS0044974' => 'camsi', 'CSS0048000' => 'camsi', 'CSS0050339' => 'camsi', 'DCAR_016320' => 'dca', 'DCAR_017203' => 'dca', 'DCAR_023665' => 'dca', 'DCAR_025613' => 'dca', 'DCAR_026729' => 'dca', 'Dinv04478' => 'din', 'Dinv21100' => 'din', 'Dinv21440' => 'din', 'Dinv23262' => 'din', 'Dinv33937' => 'din', 'Dinv34833' => 'din', 'Duzib160G0846' => 'dzi', 'Duzib192G0873' => 'dzi', 'Duzib235G1178' => 'dzi', 'Duzib248G1339' => 'dzi', 'Duzib251G0773' => 'dzi', 'Duzib268G1583' => 'dzi', 'ECA232G1891' => 'eca', 'ECA232G3592' => 'eca', 'ECA234G1519' => 'eca', 'ECA246G2146' => 'eca', 'EL10Ac2g04585' => 'bvu', 'EL10Ac3g06320' => 'bvu', 'EL10Ac6g14429' => 'bvu', 'Eucgr.B03019' => 'egr', 'Eucgr.J03137' => 'egr', 'FAN02G2422' => 'fan', 'FAN02G2709' => 'fan', 'FAN05G2022' => 'fan', 'FAN05G4802' => 'fan', 'FAN07G0481' => 'fan', 'FAN09G0034' => 'fan', 'FAN09G0890' => 'fan', 'FAN09G2681' => 'fan', 'FAN12G0856' => 'fan', 'FAN12G1493' => 'fan', 'FAN14G3228' => 'fan', 'FAN14G4170' => 'fan', 'FAN14G5168' => 'fan', 'FAN22G2053' => 'fan', 'FvH4_4g27550' => 'fve', 'FvH4_6g28060' => 'fve', 'FvH4_6g45190' => 'fve', 'Glyma.01G081500' => 'gma', 'Glyma.07G002800' => 'gma', 'Glyma.08G223800' => 'gma', 'Glyma.08G262900' => 'gma', 'Glyma.10G275100' => 'gma', 'Glyma.13G371600' => 'gma', 'Glyma.15G002002' => 'gma', 'Glyma.18G297400' => 'gma', 'Glyma.20G114700' => 'gma', 'Gohir.A06G141900' => 'ghi', 'Gohir.A09G076080' => 'ghi', 'Gohir.A10G049100' => 'ghi', 'Gohir.A13G054400' => 'ghi', 'Gohir.A13G054500' => 'ghi', 'Gohir.A13G054700' => 'ghi', 'Gohir.A13G054800' => 'ghi', 'Gohir.D06G145800' => 'ghi', 'Gohir.D09G075900' => 'ghi', 'Gohir.D10G049700' => 'ghi', 'Gohir.D13G067200' => 'ghi', 'Gohir.D13G067300' => 'ghi', 'Gohir.D13G067400' => 'ghi', 'Gohir.D13G067500' => 'ghi', 'Gorai.006G091100' => 'gra', 'Gorai.010G170000' => 'gra', 'Gorai.011G053200' => 'gra', 'Gorai.013G076500' => 'gra', 'Gorai.013G076600' => 'gra', 'Gorai.013G076800' => 'gra', 'Gorai.013G076900' => 'gra', 'GSVIVG01011907001' => 'vvi', 'GSVIVG01016076001' => 'vvi', 'GSVIVG01031048001' => 'vvi', 'HanXRQChr09g0274271' => 'han', 'HanXRQChr15g0477171' => 'han', 'HanXRQChr16g0499511' => 'han', 'HanXRQChr17g0552171' => 'han', 'HanXRQChr17g0567641' => 'han', 'Haze_14142' => 'cav', 'Haze_15240' => 'cav', 'Haze_17469' => 'cav', 'Hma1.2p1_0061F.1_g034090' => 'hma', 'Hma1.2p1_0136F.1_g062210' => 'hma', 'Hma1.2p1_0550F.1_g177380' => 'hma', 'Hma1.2p1_1774F.1_g301830' => 'hma', 'HPP92_013217' => 'vpl', 'HPP92_013218' => 'vpl', 'HPP92_013260' => 'vpl', 'HPP92_013261' => 'vpl', 'HPP92_018543' => 'vpl', 'Hund13725' => 'sun', 'Hund16138' => 'sun', 'Hund22398' => 'sun', 'Hund25077' => 'sun', 'Lalb_Chr02g0146051' => 'lal', 'Lalb_Chr04g0257401' => 'lal', 'Lalb_Chr06g0166151' => 'lal', 'Lalb_Chr10g0091191' => 'lal', 'Lalb_Chr10g0099971' => 'lal', 'Lalb_Chr17g0342101' => 'lal', 'Lalb_Chr21g0308981' => 'lal', 'Lalb_Chr24g0392791' => 'lal', 'Lj1g0010181' => 'lja', 'Lj2C443G8' => 'lonja', 'Lj2g0009720' => 'lja', 'Lj3A1017G47' => 'lonja', 'Lj3g0024342' => 'lja', 'Lj5C82T13' => 'lonja', 'Lj5g0008360' => 'lja', 'Lj6A760T49' => 'lonja', 'Lsat_1_v5_gn_3_59620' => 'lsa', 'Lsat_1_v5_gn_4_18380' => 'lsa', 'Lsat_1_v5_gn_4_84860' => 'lsa', 'Lsat_1_v5_gn_8_39020' => 'lsa', 'Manes.01G109600' => 'mes', 'Manes.02G067800' => 'mes', 'Manes.04G098700' => 'mes', 'Manes.06G069400' => 'mes', 'Manes.11G070800' => 'mes', 'Manes.14G101300' => 'mes', 'Mapoly0002s0249' => 'mpo', 'MBI07_g18991_MAGBIO' => 'mbi', 'MBI13_g10047_MAGBIO' => 'mbi', 'MBI13_g43572_MAGBIO' => 'mbi', 'MBI18_g04362_MAGBIO' => 'mbi', 'MCO15G320' => 'mco', 'MD09G1087400' => 'mdo', 'MD09G1229800' => 'mdo', 'MD13G1043000' => 'mdo', 'MD16G1043900' => 'mdo', 'MD17G1075700' => 'mdo', 'MD17G1076200' => 'mdo', 'MD17G1228500' => 'mdo', 'Medtr1g111090' => 'mtr', 'Medtr2g105410' => 'mtr', 'Medtr7g006500' => 'mtr', 'Medtr7g037380' => 'mtr', 'Medtr7g407040' => 'mtr', 'MELO3C009909.2' => 'cme', 'MELO3C012238.2' => 'cme', 'MELO3C024883.2' => 'cme', 'Migut.D01150' => 'egut', 'Migut.E00329' => 'egut', 'Migut.H00209' => 'egut', 'Migut.I00635' => 'egut', 'Migut.L00311' => 'egut', 'MSTRG.13520' => 'ama', 'MSTRG.2246' => 'ama', 'MSTRG.22836' => 'ama', 'MSTRG.830' => 'ama', 'MSTRG.9388' => 'ama', 'Nitab4.5_0000126g0020' => 'nta', 'Nitab4.5_0000280g0260' => 'nta', 'Nitab4.5_0001569g0120' => 'nta', 'Nitab4.5_0002540g0100' => 'nta', 'Nitab4.5_0003189g0010' => 'nta', 'Nitab4.5_0004194g0050' => 'nta', 'Nitab4.5_0004781g0010' => 'nta', 'Nitab4.5_0005199g0040' => 'nta', 'Nitab4.5_0005437g0030' => 'nta', 'Nitab4.5_0005737g0010' => 'nta', 'Nitab4.5_0005961g0010' => 'nta', 'Nitab4.5_0007111g0020' => 'nta', 'Nn2g12487' => 'nnu', 'Nn3g17285' => 'nnu', 'Nn3g17814' => 'nnu', 'Nn4g23813' => 'nnu', 'Nn8g40143' => 'nnu', 'Oeu003108.1' => 'oeu', 'Oeu008048.1' => 'oeu', 'Oeu030778.1' => 'oeu', 'Oeu033720.1' => 'oeu', 'Oeu033731.3' => 'oeu', 'Oeu050370.2' => 'oeu', 'Oeu051547.1' => 'oeu', 'Oeu053671.1' => 'oeu', 'Os02g0179300' => 'osa', 'Os02g0465000' => 'osa', 'Os06g0264300' => 'osa', 'Os08g0430200' => 'osa', 'Os09g0407200' => 'osa', 'Peaxi162Scf00086g00916' => 'pax', 'Peaxi162Scf00195g00121' => 'pax', 'Peaxi162Scf00314g00930' => 'pax', 'Peaxi162Scf00501g00129' => 'pax', 'Peaxi162Scf00814g00225' => 'pax', 'PGR031G1440' => 'pgr', 'PGR102G1487' => 'pgr', 'PGR119G0514' => 'pgr', 'PGSC0003DMG400012654' => 'stu', 'PGSC0003DMG400024190' => 'stu', 'PGSC0003DMG401014218' => 'stu', 'Phvul.005G184000' => 'pvu', 'Phvul.007G026400' => 'pvu', 'Phvul.007G026600' => 'pvu', 'Phvul.010G163300' => 'pvu', 'Potri.001G038000' => 'ptr', 'Potri.003G186600' => 'ptr', 'Potri.004G100700' => 'ptr', 'Potri.008G119700' => 'ptr', 'Potri.010G126200' => 'ptr', 'Potri.017G114000' => 'ptr', 'Pp3c10_8490' => 'ppa', 'Pp3c18_16750' => 'ppa', 'Pp3c18_16820' => 'ppa', 'Pp3c21_190' => 'ppa', 'Pp3c21_210' => 'ppa', 'PRCOL_00001791' => 'pco', 'Prupe.1G309400' => 'ppe', 'Prupe.1G309600' => 'ppe', 'Prupe.3G105900' => 'ppe', 'Prupe.3G238000' => 'ppe', 'Psat0s2789g0040' => 'psa', 'Psat3g205600' => 'psa', 'Psat5g308200' => 'psa', 'Psat6g228880' => 'psa', 'PSO017G0864' => 'pso', 'PSO063G1100' => 'pso', 'PSO063G3886' => 'pso', 'PSO478G1116' => 'pso', 'PSO509G0009' => 'pso', 'PSO782G3663' => 'pso', 'PSO782G5484' => 'pso', 'QL02p051988' => 'qlo', 'QL02p052021' => 'qlo', 'QL05p081609' => 'qlo', 'RcHm_v2.0_Chr1g0327471' => 'rch', 'RcHm_v2.0_Chr2g0131831' => 'rch', 'RcHm_v2.0_Chr2g0162901' => 'rch', 'RcHm_v2.0_Chr4g0435391' => 'rch', 'Rhsim08G0201400' => 'rsi', 'Rhsim08G0201700' => 'rsi', 'Rhsim08G0201800' => 'rsi', 'Rhsim08G0202000' => 'rsi', 'Rhsim08G0202200' => 'rsi', 'Rhsim09G0109100' => 'rsi', 'Rhsim10G0023600' => 'rsi', 'Rhsim12G0083000' => 'rsi', 'Sabra01G0026600' => 'sbr', 'Sabra03G0136700' => 'sbr', 'Sabra04G0079300' => 'sbr', 'Sabra10G0095900' => 'sbr', 'SalBow8G3482' => 'sbo', 'SalBow8G4417' => 'sbo', 'Sc10g0001230' => 'sci', 'Sc10g0006480' => 'sci', 'Sc11g0008270' => 'sci', 'Sc14g0007520' => 'sci', 'Sed0001035' => 'sed', 'Sed0005465' => 'sed', 'Sed0008781' => 'sed', 'Sed0016702' => 'sed', 'Sed0022782' => 'sed', 'Sed0024821' => 'sed', 'SEGI_09049' => 'sgi', 'SEGI_09322' => 'sgi', 'SEGI_18077' => 'sgi', 'SEGI_30054' => 'sgi', 'SEGI_35711' => 'sgi', 'SGA_v2.0_scaffold14G06852' => 'sas', 'SGA_v2.0_scaffold170G38752' => 'sas', 'SGA_v2.0_scaffold2G00991' => 'sas', 'SGA_v2.0_scaffold2G01106' => 'sas', 'SGA_v2.0_scaffold2G01132' => 'sas', 'SGA_v2.0_scaffold5G02834' => 'sas', 'SHI11333' => 'shi', 'SMO353G0381' => 'smo', 'SMO364G0855' => 'smo', 'Solyc02g063130.4' => 'sly', 'Solyc02g063133.1' => 'sly', 'Solyc02g085840.2' => 'sly', 'Solyc03g117780.2' => 'sly', 'Solyc04g007120.4' => 'sly', 'Sopen02g014200' => 'spe', 'Sopen02g030530' => 'spe', 'Sopen03g036690' => 'spe', 'Sopen04g002210' => 'spe', 'Sp1g14430' => 'spa', 'Sp3g01570' => 'spa', 'Sp5g34720' => 'spa', 'Sp7g03580' => 'spa', 'TAR371G1262' => 'tar', 'TAR622G0705' => 'tar', 'TAR625G1188' => 'tar', 'TAR629G2621' => 'tar', 'THA.LOC104803002' => 'tha', 'THA.LOC104808161' => 'tha', 'THA.LOC104820952' => 'tha', 'THA.LOC104822643' => 'tha', 'THA.LOC104823864' => 'tha', 'Thecc.02G356500' => 'tca', 'Thecc.04G135400' => 'tca', 'Thecc.06G133500' => 'tca', 'Thhalv10007982m.g' => 'esa', 'Thhalv10016009m.g' => 'esa', 'Thhalv10018655m.g' => 'esa', 'Thhalv10020817m.g' => 'esa', 'Thhalv10027790m.g' => 'esa', 'TPR.G11095' => 'tpr', 'TPR.G26274' => 'tpr', 'TPR.G9716' => 'tpr', 'TWI53G1625' => 'twi', 'TWI74G1005' => 'twi', 'TWI74G1388' => 'twi', 'TWI75G1180' => 'twi', 'TWI77G0519' => 'twi', 'unitig_22.g6872' => 'ugi', 'unitig_52.g17031' => 'ugi', 'unitig_747.g21197' => 'ugi', 'unitig_747.g21198' => 'ugi', 'unitig_8.g3444' => 'ugi', 'unitig_8.g3445' => 'ugi', 'vmacro01376' => 'vma', 'vmacro05561' => 'vma', 'vmacro05562' => 'vma', 'vmacro10552' => 'vma', 'vmacro19082' => 'vma', 'VMungo0331G0148' => 'vmu', 'VMungo0578G0001' => 'vmu', 'VMungo0720G2089' => 'vmu', 'VMungo1080G1097' => 'vmu', 'VMungo1309G2748' => 'vmu', 'Zm00001eb099280' => 'zma', 'Zm00001eb206650' => 'zma', 'Zm00001eb280580' => 'zma', 'Zm00001eb312260' => 'zma', 'Zm00001eb379990' => 'zma' ) $gf_id = 'HOM05D001266' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001266' ) $data_identifier = 'HOM05D001266' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 10, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 14, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb379990' $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